Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1565
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42999
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:16106 original size:17 final size:17
Alignment explanation
Indices: 16081--16130 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
16071 TGTAAATAAT
16081 AACTACTAGAAATCATA
1 AACTACTAGAAATCATA
*
16098 AATTACTAGAAATC--A
1 AACTACTAGAAATCATA
16113 AACTACTAGAAATCATA
1 AACTACTAGAAATCATA
16130 A
1 A
16131 TTAGCTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 14 0.48
17 15 0.52
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (17 bp):
AACTACTAGAAATCATA
Found at i:16121 original size:15 final size:15
Alignment explanation
Indices: 16081--16127 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
16071 TGTAAATAAT
16081 AACTACTAGAAATCATA
1 AACTACTAGAAATC--A
*
16098 AATTACTAGAAATCA
1 AACTACTAGAAATCA
16113 AACTACTAGAAATCA
1 AACTACTAGAAATCA
16128 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.54
17 13 0.46
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.23
Consensus pattern (15 bp):
AACTACTAGAAATCA
Found at i:17888 original size:28 final size:28
Alignment explanation
Indices: 17856--17911 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
17846 TTTTGACTAG
17856 TAGGAGTAATATTAGAGGTGAAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
*
17884 TAGGAGTAATATTAGAGGTGCAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
17912 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (28 bp):
TAGGAGTAATATTAGAGGTGAAAAAATT
Found at i:21222 original size:21 final size:22
Alignment explanation
Indices: 21196--21236 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21186 CAAGTCTATC
*
21196 AAATAAACATA-AACTTCAAAG
1 AAATAAACATACAAATTCAAAG
*
21217 AAATAAGCATACAAATTCAA
1 AAATAAACATACAAATTCAA
21237 CCATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.15, G:0.05, T:0.20
Consensus pattern (22 bp):
AAATAAACATACAAATTCAAAG
Found at i:21873 original size:41 final size:42
Alignment explanation
Indices: 21816--21897 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
21806 AATGGCCCTG
* * *
21816 CTCACACGAGCTGTGGGTCGGCATGT-AGCTACACGATGCTA
1 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
21857 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCT
1 CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCT
21898 GCTTACACGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 23 0.62
42 14 0.38
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (42 bp):
CTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
Found at i:21914 original size:42 final size:41
Alignment explanation
Indices: 21813--21914 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 41
21803 TGAAATGGCC
* *
21813 CTGCTCACACGAGCTGTGGGTCGGCATGTAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
* *
21854 CTACTCACACAAGCTGTGGGTCAGAATGTAAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGT-AGCTACACGATG
* *
21896 CTGCTTACACGAGTTGTGG
1 CTGCTCACACGAGCTGTGG
21915 AGAATTCACA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 25 0.48
42 27 0.52
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (41 bp):
CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
Found at i:31523 original size:17 final size:17
Alignment explanation
Indices: 31501--31535 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31491 CATAGATATT
31501 AACTAACACAAAAATAA
1 AACTAACACAAAAATAA
**
31518 AACTAATGCAAAAATAA
1 AACTAACACAAAAATAA
31535 A
1 A
31536 TACATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (17 bp):
AACTAACACAAAAATAA
Found at i:39917 original size:68 final size:71
Alignment explanation
Indices: 39775--40018 Score: 228
Period size: 68 Copynumber: 3.4 Consensus size: 71
39765 TGATTCCGCC
* * * *
39775 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAGTGCTGATTCCACCATATTT
1 AAGGGGTTGCTAAGTGCTGATTCCCC---TCATAGGTGGTTGCTAGTGCTGATCCCACCATATCT
39840 TAAATGTG-
63 TAAATGTGA
*
39848 AAGGGGTTGCTAAGTGCTGATTCCCC-CA-AGG-GGTTGCTAAGTGCTGATCCCACCGTATCTTA
1 AAGGGGTTGCTAAGTGCTGATTCCCCTCATAGGTGGTTGCT-AGTGCTGATCCCACCATATCTTA
39910 AATGTGA
65 AATGTGA
* * * **
39917 AAGGGGTTGTTAAGTGCTGATTCCCCGATTCACT-GGTGGTTGCTAAGTGTTGATTCCACTGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCC---TCA-TAGGTGGTTGCT-AGTGCTGATCCCACCATA-
* *
39981 TTTTGAATGTGAA
60 TCTTAAATGTG-A
* *
39994 AAAGGGTTGCTAAGTGTTGATTCCC
1 AAGGGGTTGCTAAGTGCTGATTCCC
40019 TGAATCATTG
Statistics
Matches: 146, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
67 7 0.05
68 28 0.19
69 27 0.18
73 27 0.18
74 2 0.01
75 23 0.16
76 9 0.06
77 23 0.16
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (71 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCTCATAGGTGGTTGCTAGTGCTGATCCCACCATATCTTAA
ATGTGA
Found at i:40008 original size:77 final size:75
Alignment explanation
Indices: 39775--40054 Score: 333
Period size: 77 Copynumber: 3.8 Consensus size: 75
39765 TGATTCCGCC
* *
39775 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCT-AGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
39839 TTAAATGTG-
66 TTAAATGTGA
* * *
39848 AAGGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
39907 TTAAATGTGA
66 TTAAATGTGA
* * * *
39917 AAGGGGTTGTTAAGTGCTGATTCCCCGATTCACTGGTGGTTGCTAAGTGTTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
*
39982 TTTGAATGTGAA
65 TTTAAATGTG-A
* * * * * * *
39994 AAAGGGTTGCTAAGTGTTGATTCCCTGAATCATTGGTTGTTGCTACGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
40055 AAAACGGATA
Statistics
Matches: 174, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
67 7 0.04
68 28 0.16
69 27 0.16
73 27 0.16
74 2 0.01
75 23 0.13
76 9 0.05
77 51 0.29
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGA
Done.